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标题: orca计算mpirun报错 [打印本页]

作者
Author: JefferSon 时间: 2023-3-16 19:37
标题: orca计算mpirun报错
Sob老师和各位老师好，

我在算一个小分子激发态的荧光，然后输入文件如下所示。

! PBE0 def2-SV(P) def2/J def2-SVP/C RIJCOSX tightSCF opt freq noautostart miniprint nopop
%maxcore  1000
%pal nprocs  16 end
%tddft
nroots 10
mode riints_disk
end
* xyz 0 1

如果我在命令行输入 orca /home/zhangfusheng/Desktop/MLB/orca/PYACR_pls108.inp > /home/zhangfusheng/Desktop/MLB/orca/PYACR_pls108.out
他会报错
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[41725,1],12]
  Exit code: 1
--------------------------------------------------------------------------
[root@125-217-250-4 orca]# orca /home/zhangfusheng/Desktop/MLB/orca/PYACR_pls108                                                                            .inp > /home/zhangfusheng/Desktop/MLB/orca/PYACR_pls108.out
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: /root/Downloads/orca/orca_gtoint_mpi
Node: 125-217-250-4

while attempting to start process rank 0.
--------------------------------------------------------------------------
[file orca_tools/qcmsg.cpp, line 465]:
  .... aborting the run

然后我在命令行输入了  mpirun -np 16 orca /home/zhangfusheng/Desktop/MLB/orca/PYACR_pls108.inp > /home/zhangfusheng/Desktop/MLB/orca/PYACR_pls108.out

然后mpirun报错
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[41725,1],12]
  Exit code: 1
--------------------------------------------------------------------------

但是我用核数为1 时，程序能正常启动，感谢大家的答疑解惑，祝大家工作顺利，生活愉快！

然后每次出错前都会显示
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/orca.py:52: PyGIWarning: Gtk was imported without specifying a version first. Use gi.require_version('Gtk', '3.0') before import to ensure that the right version gets loaded.
  from gi.repository import Gtk
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck
/usr/lib64/python2.7/site-packages/orca/mouse_review.py:31: PyGIWarning: Wnck was imported without specifying a version first. Use gi.require_version('Wnck', '3                                                                            .0') before import to ensure that the right version gets loaded.
  from gi.repository import Wnck

作者
Author: wzkchem5 时间: 2023-3-16 20:30
检查openmpi安装是否错误，尤其是相关的环境变量有没有设置正确
此外注意orca不能用mpirun调用，如何调用orca做并行计算在orca说明书里都写了
最后那个问题应该是PATH变量设置错误，导致调用成linux自带的一个叫orca的工具了。

作者
Author: JefferSon 时间: 2023-3-16 21:56
本帖最后由 JefferSon 于 2023-3-16 22:05 编辑

wzkchem5 发表于 2023-3-16 20:30
检查openmpi安装是否错误，尤其是相关的环境变量有没有设置正确
此外注意orca不能用mpirun调用，如何调用o ...

老师您好，感谢您的回复。
我之前的安装应该是成功的，并没有报错且mpiexec也显示4.1.1。我将给Fortran升级至7.3.1后重新编译和安装了openmpi，也是并没有报错并且mpeexec显示4.1.1。依旧显示如下报错。我怀疑是ORCA的问题，我现在去重新下载share版并解压康康。十分感谢您的答疑解惑，祝工作顺利！

至于环境变量我是这样输入的：
export PATH=/root/Downloads/orca:$PATH
export LD_LIBRARY_PATH=/root/Downloads/orca:$LD_LIBRARY_PATH
export PATH=/root/Downloads/openmpi411/bin:$PATH
export LD_LIBRARY_PATH=/root/Downloads/openmpi411/lib:$LD_LIBRARY_PATH
export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
alias orca='/root/Downloads/orca/orca'

报错
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: /root/Downloads/orca/orca_gtoint_mpi
Node: 125-217-250-4

while attempting to start process rank 0.
--------------------------------------------------------------------------
[file orca_tools/qcmsg.cpp, line 465]:
.... aborting the run

作者
Author: JefferSon 时间: 2023-3-16 22:11

JefferSon 发表于 2023-3-16 21:56
老师您好，感谢您的回复。
我之前的安装应该是成功的，并没有报错且mpiexec也显示4.1.1。我将给Fortran ...

成功了，再次谢谢老师，下载的orca版本shared版本可以，那几个part123版本的我不行，再次谢谢老师的帮助和耐心指导！祝工作顺利，生活愉快！

作者
Author: 渡边京介 时间: 2023-11-11 00:04
您好请问您现在的脚本写法是什么样子的只需要换一个orca版本就可以了吗

作者
Author: JefferSon 时间: 2023-12-22 00:34

渡边京介发表于 2023-11-11 00:04
您好请问您现在的脚本写法是什么样子的只需要换一个orca版本就可以了吗

是版本的问题我后续更换了orca版本后，直接以orca /home/zhangfusheng/Desktop/MLB/orca/PYACR_pls108.inp > /home/zhangfusheng/Desktop/MLB/orca/PYACR_pls108.out 即可运行

作者
Author: zjxitcc 时间: 2023-12-22 09:46

渡边京介发表于 2023-11-11 00:04
您好请问您现在的脚本写法是什么样子的只需要换一个orca版本就可以了吗

（1）那是题主环境变量没写对。只需用动态库版本即可(ORCA 5.0.4, Linux, x86-64, shared-version, .tar.xz Archive)，完全不需尝试其他版本。
（2）如果提交到当前节点进行计算，不需要使用脚本，运行诸如orca h2o.inp >h2o.out 2>&1即可；如果提交到超算队列，那往往要用脚本，脚本内容取决于队列要求和队列特点，无法一概而论，应咨询超算集群管理员。注意，ORCA输入文件.inp不叫脚本。

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